This invention relates to inhibitors of bacterial ribonuclease P holoenzymes. Such inhibitors are useful as antibacterial agents.
Ribonuclease P (RNase P) is an endoribonuclease that cleaves the 5′-terminal leader sequences of precursor tRNAs. RNase P has been characterized in a representative number of species.
In bacteria, the structure of the RNase P holoenzyme is composed of a catalytic RNA subunit (350-450 nucleotides; encoded by the rnp B gene) and a single protein subunit (110-160 amino acids; encoded by the rnp A gene); both are essential for in vivo activity. In Escherichia coli (E. coli), the RNA subunit is termed M1 and the protein subunit is C5. The C5 protein engages in specific interactions with the M1 RNA to stabilize certain M1 RNA conformations. Through these interactions with M1, C5 plays a critical role in the recognition/binding of some substrates.
Comparison of RNase P protein subunits between bacterial species reveals that their primary structures have only a moderate degree of identity. For example, the protein subunits of Bacillus subtilis (B. subtilis) and E. coli are 30% identical. The functional significance of some conserved amino acid residues has been confirmed by mutagenesis studies which have shown that these conserved amino acids play a significant role in the catalytic function of the RNase P holoenzyme.
The tertiary structure of the RNase P protein subunit expressed in B. subtilis has been determined by X-ray crystallography. The overall topology of α-helices and β-sheets is α1 β2 β3 α2 β4 α3, with an uncommon β3α2β4 cross-over connection that may confer specific functional consequences. Another functional aspect of the protein is the long loop connecting β2 to β3, termed the metal binding loop, which binds Zn2+ ions and mediates interlattice contacts. In addition, the crystal structure reveals an overall fold that is similar to the ribosomal protein S5, translational elongation factor EF-G (domain IV), and DNA gyrase.
Many pathogens exist for which there are few effective treatments, and the number of strains resistant to available drugs is continually increasing. Thus, improved methods are needed for the treatment and prevention of infections caused by a number of bacteria. Desirably, these treatments kill pathogenic bacteria without harming the tissues of the infected patient.